surface-catalysis

name	surface-catalysis
description	Use when the user asks about surface slabs, Miller indices, adsorbate placement, adsorption sites, water layers, passivation, heterostructures, lattice matching, moire bilayers, or catalysis workflows.

Surface & Catalysis Workflow

Surface Slab Generation

1. Start with a bulk crystal (fetch or use current)
2. catgo_generate_slab with miller_index as [h, k, l]
   • Defaults: min_slab_size=10.0 A, min_vacuum_size=15.0 A
   • Returns all symmetrically distinct terminations
3. Inspect result with catgo_structure_info

Miller index selection:

Surface	Miller Index	Common Use
FCC (111)	[1,1,1]	Close-packed, catalysis
FCC (100)	[1,0,0]	Open surface
BCC (110)	[1,1,0]	Close-packed
Rutile (110)	[1,1,0]	TiO2 catalysis
Perovskite (001)	[0,0,1]	ABO3 surfaces

Adsorbate Placement

1. catgo_adsorption_sites — Find top, bridge, hollow sites. height default 2.0 A.
2. catgo_adsorption_place — Place adsorbate at chosen site coordinates.

Get adsorbate molecules via catgo_fetch_molecule:

• CO, CO2, H2O, NH3, O2, CH4, etc.

Surface Passivation

catgo_passivate — Cap dangling bonds with pseudo-hydrogen on slab bottom surface. Requires both slab and bulk reference structure dicts.

Water Layer

catgo_water_layer — Add TIP4P water layer for solid/liquid interface models. Parameters: z_start, z_end, min_distance (overlap removal), equilibrate (optional LAMMPS).

Heterostructure & Interface

ZSL Lattice Matching (Two-Step)

1. catgo_hetero_search — Find lattice-matched substrate/film pairs
2. catgo_hetero_build — Build interface from selected match

One-Step Interface

catgo_hetero_build_intermat — Simpler pipeline, less control but faster prototyping.

Moire Bilayer

1. catgo_moire_search — Find commensurate twist angles with supercell sizes
2. catgo_moire_build — Build bilayer at selected angle

Complete Catalysis Recipe

1. catgo_fetch_crystal (bulk, e.g. Pt)
2. catgo_generate_slab (miller_index=[1,1,1], min_slab_size=12, min_vacuum_size=15)
3. catgo_passivate (bottom surface)
4. catgo_adsorption_sites (find sites)
5. catgo_fetch_molecule (get adsorbate)
6. catgo_adsorption_place (place at chosen site)
7. catgo_structure_info (verify)
8. Generate DFT input (see computational-input skill)